Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004605.1 Hibiscus syriacus cultivar Beakdansim tig00010294_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 86285
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:412 original size:20 final size:22
Alignment explanation
Indices: 374--413 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
364 TTTAGTAGAA
374 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
396 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
414 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:3378 original size:20 final size:18
Alignment explanation
Indices: 3322--3378 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 18
3312 TATATTTTCC
*
3322 AACAATTGGTTATCTTCTT
1 AACAATTGG-TATCTTTTT
*
3341 AACAATTAGTATCCTTTTGT
1 AACAATTGGTAT-CTTTT-T
3361 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
3379 CATTAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 4 0.12
19 17 0.52
20 12 0.36
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (18 bp):
AACAATTGGTATCTTTTT
Found at i:3556 original size:29 final size:30
Alignment explanation
Indices: 3488--3546 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3478 AATTTAAGGC
3488 AAAATGGTTTTTGGACTTGAATTAAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTAAATTTAA
3519 AAAATGTTTTTGGACTT-AATTAAATTTA
1 AAAATGTTTTTGGACTTGAATTAAATTTA
3547 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTAAATTTAA
Found at i:3851 original size:20 final size:22
Alignment explanation
Indices: 3813--3852 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3803 TTTGAGTAGA
3813 AAAATCATCCCCAAACGGCTTC
1 AAAATCATCCCCAAACGGCTTC
3835 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
3853 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTTC
Found at i:4325 original size:23 final size:23
Alignment explanation
Indices: 4293--4350 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
4283 CCTAAACACA
*
4293 AAACCGTTCCGACCCCTCTTTGC
1 AAACCATTCCGACCCCTCTTTGC
4316 AAACCATTCCGACCCCTCTTTGC
1 AAACCATTCCGACCCCTCTTTGC
4339 AAACCATTCCGA
1 AAACCATTCCGA
4351 TTGTCGATTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.41, G:0.10, T:0.24
Consensus pattern (23 bp):
AAACCATTCCGACCCCTCTTTGC
Found at i:5522 original size:25 final size:25
Alignment explanation
Indices: 5488--5540 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5478 TACATAGGAG
5488 AACATCTATAAATGTATATTAAACT
1 AACATCTATAAATGTATATTAAACT
5513 AACATCTATAAATGTATATTAAACT
1 AACATCTATAAATGTATATTAAACT
5538 AAC
1 AAC
5541 TTTTTCAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (25 bp):
AACATCTATAAATGTATATTAAACT
Found at i:7344 original size:23 final size:24
Alignment explanation
Indices: 7305--7354 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
7295 TTTATATGTA
7305 ATAATTAATTAATAA-TTT-AAAT
1 ATAATTAATTAATAATTTTAAAAT
7327 ATAATTTAACTTAA-AATTTTAAAAT
1 ATAA-TTAA-TTAATAATTTTAAAAT
7352 ATA
1 ATA
7355 TATAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 7 0.29
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTAATTAATAATTTTAAAAT
Found at i:7965 original size:2 final size:2
Alignment explanation
Indices: 7958--8062 Score: 85
Period size: 2 Copynumber: 53.5 Consensus size: 2
7948 ATGTTTAATG
*
7958 AT AT AT AT AT AT AT AT AT ACT -T AT AT AT -T AT ACT TT AT ACT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT A-T
* * * * * *
7999 -T AT AT AT AT TT AT AT AC AC AC AT AT AT AT AA AT A- AT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8038 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8063 AAAAACTATA
Statistics
Matches: 86, Mismatches: 9, Indels: 16
0.77 0.08 0.14
Matches are distributed among these distances:
1 5 0.06
2 78 0.91
3 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8154 original size:35 final size:37
Alignment explanation
Indices: 8115--8212 Score: 100
Period size: 37 Copynumber: 2.8 Consensus size: 37
8105 TGTATGGTTT
*
8115 TATATAT-TATAT-TTTATATA-AGTATATACTTATAA
1 TATATATGTATATGTATATATATA-TATATACTTATAA
* *
8150 TATATATGTGTGTGTATATATATATATATACTTATAA
1 TATATATGTATATGTATATATATATATATACTTATAA
*
8187 TATA-A-GTATAGTGTACAT-TATATATA
1 TATATATGTATA-TGTATATATATATATA
8213 CATGCATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
35 18 0.34
36 10 0.19
37 24 0.45
38 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (37 bp):
TATATATGTATATGTATATATATATATATACTTATAA
Found at i:8158 original size:51 final size:56
Alignment explanation
Indices: 8086--8196 Score: 144
Period size: 51 Copynumber: 2.1 Consensus size: 56
8076 ATACTTGTAT
* *
8086 TATATACTTATAAGTATTATGTATG-GT-TTTATATAT-TATA-TT-TTATATAAG
1 TATATACTTATAAGTATTATGTATGTGTATATATATATATATACTTATAATATAAG
*
8137 TATATACTTATAA-TATATATGTGTGTGTATATATATATATATACTTATAATATAAG
1 TATATACTTATAAGTAT-TATGTATGTGTATATATATATATATACTTATAATATAAG
8193 TATA
1 TATA
8197 GTGTACATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
50 3 0.06
51 20 0.39
52 2 0.04
53 8 0.16
54 4 0.08
55 2 0.04
56 12 0.24
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.50
Consensus pattern (56 bp):
TATATACTTATAAGTATTATGTATGTGTATATATATATATATACTTATAATATAAG
Found at i:8209 original size:37 final size:38
Alignment explanation
Indices: 8128--8212 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 38
8118 ATATTATATT
* *
8128 TTATATAAGTATATACTTATAATATATATGTGTGTGTATA
1 TTATAT-A-TATATACTTATAATATATATGTATGTGTACA
8168 -TATATATATATACTTATAATATA-A-GTATAGTGTACA
1 TTATATATATATACTTATAATATATATGTAT-GTGTACA
8204 TTATATATA
1 TTATATATA
8213 CATGCATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 3 0.07
36 7 0.17
37 25 0.61
38 1 0.02
39 5 0.12
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (38 bp):
TTATATATATATACTTATAATATATATGTATGTGTACA
Found at i:8229 original size:23 final size:23
Alignment explanation
Indices: 8203--8258 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
8193 TATAGTGTAC
*
8203 ATTATATATACATGCATTAT-CAT
1 ATTATATA-ACATGCATCATACAT
* *
8226 ATTATCATAACATTCATCATACGT
1 ATTAT-ATAACATGCATCATACAT
8250 ATTATATAA
1 ATTATATAA
8259 TATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTATATAACATGCATCATACAT
Found at i:8263 original size:2 final size:2
Alignment explanation
Indices: 8252--8281 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8242 TCATACGTAT
8252 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8282 TAAAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9256 original size:20 final size:20
Alignment explanation
Indices: 9233--9298 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
9223 ATCAGTTAAA
*
9233 TTATTAAAATAATATTATTT
1 TTATAAAAATAATATTATTT
*
9253 TTATAAAAATAGTACTTAATTT
1 TTATAAAAATAATA-TT-ATTT
*
9275 TT-TAAAAATAACATCTATTT
1 TTATAAAAATAATAT-TATTT
9295 TTAT
1 TTAT
9299 CATATAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 19 0.50
21 13 0.34
22 6 0.16
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
TTATAAAAATAATATTATTT
Found at i:9465 original size:22 final size:22
Alignment explanation
Indices: 9412--9467 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
9402 CATATCCCTC
*
9412 ATCTCTACTATACAGTATCTCT
1 ATCTCTACTCTACAGTATCTCT
*
9434 ATCTATACTCTACAGTATCTCT
1 ATCTCTACTCTACAGTATCTCT
9456 ATCTCTACTCTA
1 ATCTCTACTCTA
9468 AAGATGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.41
Consensus pattern (22 bp):
ATCTCTACTCTACAGTATCTCT
Found at i:12411 original size:17 final size:17
Alignment explanation
Indices: 12389--12422 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12379 TTACATTCAC
12389 TTTATAATTATATGCAT
1 TTTATAATTATATGCAT
12406 TTTATAATTATATGCAT
1 TTTATAATTATATGCAT
12423 GGACAGACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTATAATTATATGCAT
Found at i:15116 original size:54 final size:55
Alignment explanation
Indices: 15027--15130 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 55
15017 TTTTCTGCAC
* *
15027 TGTTTCAATTCAATCTTTACATTCTGATTTCTTTC-ATTCTAGT-CCTTTACTCAA
1 TGTTTCAATTCAATCTTTACATTCTAATTTATTTCAATT-TAGTCCCTTTACTCAA
* * *
15081 TGTTTTAATTTCAA-CTTTGCATTTTAATTTATTTCAATTTAGTCCCTTTA
1 TGTTTCAA-TTCAATCTTTACATTCTAATTTATTTCAATTTAGTCCCTTTA
15131 TATTTATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
54 28 0.67
55 14 0.33
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (55 bp):
TGTTTCAATTCAATCTTTACATTCTAATTTATTTCAATTTAGTCCCTTTACTCAA
Found at i:15141 original size:33 final size:30
Alignment explanation
Indices: 15101--15186 Score: 86
Period size: 33 Copynumber: 2.8 Consensus size: 30
15091 TCAACTTTGC
*
15101 ATTTTAATTTATTTCAATTTAGTCCCTTTA
1 ATTTTAATTTATTTAAATTTAGTCCCTTTA
* * *
15131 TATTTATTAATTTCTTTTAATTTTGT--CTTTA
1 -A-TT-TTAATTTATTTAAATTTAGTCCCTTTA
*
15162 ATTTTAATTTATTTAAATCTAGTCC
1 ATTTTAATTTATTTAAATTTAGTCC
15187 TAGAATTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
28 16 0.36
29 2 0.05
30 1 0.02
31 6 0.14
32 2 0.05
33 17 0.39
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.59
Consensus pattern (30 bp):
ATTTTAATTTATTTAAATTTAGTCCCTTTA
Found at i:17255 original size:35 final size:35
Alignment explanation
Indices: 17209--17284 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
17199 AAAACAGTCC
* *
17209 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
17244 TCAATTTCATTCTCAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
17279 TCAATT
1 TCAATT
17285 CAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:17827 original size:130 final size:130
Alignment explanation
Indices: 17681--17928 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
17671 TATTTATATA
* ** *
17681 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* *
17746 TTAGCACATGATCATGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
17811 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
* *
17876 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTA
17929 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATG
TTAACACATGATCATGACATATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:17901 original size:23 final size:21
Alignment explanation
Indices: 17855--17901 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
17845 AATTAATCAT
17855 TTAACCAGGATCTGACATATG
1 TTAACCAGGATCTGACATATG
* *
17876 TTAACACATGATCATGATATATG
1 TTAAC-CAGGATC-TGACATATG
17899 TTA
1 TTA
17902 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATATG
Found at i:17959 original size:130 final size:129
Alignment explanation
Indices: 17695--17959 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
17685 ATTTGGTCCT
* ** * *
17695 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* *** * * **** *
17760 TGACATGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
17825 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
* * *
17890 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACATATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
17954 -A
128 CA
17955 AAATT
1 AAATT
17960 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATATGTTAACACATGATCA
TGACATATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:22228 original size:36 final size:36
Alignment explanation
Indices: 22186--22261 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
22176 TTATAGCTAA
*
22186 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
22222 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
22258 AAAA
1 AAAA
22262 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:26743 original size:15 final size:15
Alignment explanation
Indices: 26725--26754 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26715 CCACGGTGCT
26725 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
26740 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
26755 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:27215 original size:34 final size:35
Alignment explanation
Indices: 27177--27251 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
27167 TATAGCTAAA
*
27177 AAAATCGTCTTTATTCGAA-TTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
27211 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
27246 AAAATC
1 AAAATC
27252 CCGAAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 18 0.46
35 21 0.54
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (35 bp):
AAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:32057 original size:11 final size:11
Alignment explanation
Indices: 32041--32066 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
32031 TTAAATTATA
32041 TATATATAATT
1 TATATATAATT
32052 TATATATAATT
1 TATATATAATT
32063 TATA
1 TATA
32067 GGAGTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATATAATT
Found at i:34875 original size:37 final size:37
Alignment explanation
Indices: 34802--34876 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
34792 TTAGAAAAAT
* *
34802 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
34839 ATTTATATATTTTTTTTTACAAAAA-TGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTA-AAAAATTGAAAATCATAAA
34876 A
1 A
34877 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 15 0.45
38 13 0.39
39 5 0.15
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:35730 original size:60 final size:60
Alignment explanation
Indices: 35590--35730 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 60
35580 TTTTTTATTT
* * * *
35590 TAAATTAGTCTCTAAACTTTCAAATATTTTAATTTCATCCTTAGATAATGACTATTATTT
1 TAAATTAGTCTCTAAACTTTTAAATATTTTAATTTCATCCTTAAATAATGACTATCATTC
35650 TAAATTAGTC-CTCAAACTTTTAAATATTTTAATTTCAT-CTCTAAACT-ATGAACT-TCATTC
1 TAAATTAGTCTCT-AAACTTTTAAATATTTTAATTTCATCCT-TAAA-TAATG-ACTATCATTC
* *
35710 TAAATTGGTCTCTGAACTTTT
1 TAAATTAGTCTCTAAACTTTT
35731 TGAACATTCA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
59 4 0.06
60 60 0.86
61 6 0.09
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (60 bp):
TAAATTAGTCTCTAAACTTTTAAATATTTTAATTTCATCCTTAAATAATGACTATCATTC
Found at i:36127 original size:38 final size:37
Alignment explanation
Indices: 36045--36129 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 37
36035 TAGATTTTTG
36045 TCAACCCGATATGACCCAAAAATTATACACCTTCTACT
1 TCAACCCGA-ATGACCCAAAAATTATACACCTTCTACT
*
36083 T-GACCCGAATCCGACCCGAAAAA-TATACACTCTTC-A-T
1 TCAACCCGAAT--GACCC-AAAAATTATACAC-CTTCTACT
36120 TCAACCCGAA
1 TCAACCCGAA
36130 CTCAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
36 2 0.05
37 8 0.20
38 21 0.52
39 9 0.22
ACGTcount: A:0.36, C:0.33, G:0.08, T:0.22
Consensus pattern (37 bp):
TCAACCCGAATGACCCAAAAATTATACACCTTCTACT
Found at i:40580 original size:21 final size:22
Alignment explanation
Indices: 40556--40598 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40546 ATAAATATGA
40556 TTAAAAATA-TTAATTATTTTT
1 TTAAAAATATTTAATTATTTTT
* *
40577 TTAAAATTATTTATTTATTTTT
1 TTAAAAATATTTAATTATTTTT
40599 AATAGAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAAAAATATTTAATTATTTTT
Found at i:44795 original size:35 final size:35
Alignment explanation
Indices: 44740--44859 Score: 177
Period size: 35 Copynumber: 3.4 Consensus size: 35
44730 GATTTGTATC
*
44740 GCTTAACTACTCTTCCATGAAGGCTAAATTGCATT
1 GCTTCACTACTCTTCCATGAAGGCTAAATTGCATT
* *
44775 GCTTCACTACTCTTCTATGAAGGCTAGATTGCATT
1 GCTTCACTACTCTTCCATGAAGGCTAAATTGCATT
* * *
44810 GCTTCACTACTCTTCCGTGAAGGCTGGATTTGCATT
1 GCTTCACTACTCTTCCATGAAGGCT-AAATTGCATT
44846 GCTTCACTACTCTT
1 GCTTCACTACTCTT
44860 TTGTGAAGGC
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
35 55 0.72
36 21 0.28
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (35 bp):
GCTTCACTACTCTTCCATGAAGGCTAAATTGCATT
Found at i:44843 original size:71 final size:70
Alignment explanation
Indices: 44740--44875 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 70
44730 GATTTGTATC
44740 GCTTAACTACTCTTCCATGAAGGCTAAATTGCATTGCTTCACTACTCTTCTATGAAGGCTAGATT
1 GCTTAACTACTCTTCCATGAAGGCTAAATTGCATTGCTTCACTACTCTTCTATGAAGGCTAGATT
44805 GCATT
66 GCATT
* * * * * * *
44810 GCTTCACTACTCTTCCGTGAAGGCTGGATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTGGAT
1 GCTTAACTACTCTTCCATGAAGGCT-AAATTGCATTGCTTCACTACTCTTCTATGAAGGCTAGAT
44875 T
65 T
44876 CGAATGACTT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
70 23 0.40
71 35 0.60
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (70 bp):
GCTTAACTACTCTTCCATGAAGGCTAAATTGCATTGCTTCACTACTCTTCTATGAAGGCTAGATT
GCATT
Found at i:46128 original size:39 final size:39
Alignment explanation
Indices: 46073--46153 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
46063 TTTCATATGG
* *
46073 ATTATTTATGTCTGATATGAG-CTTTCAATATGCCCCAAC
1 ATTATTTATGTCTGATATAAGTC-TTCAAGATGCCCCAAC
*
46112 ATTATTTCATGT-TGATATAAGTCTTCAAGATGTCCCAAC
1 ATTATTT-ATGTCTGATATAAGTCTTCAAGATGCCCCAAC
46151 ATT
1 ATT
46154 CTAAGTTGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 32 0.86
40 5 0.14
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (39 bp):
ATTATTTATGTCTGATATAAGTCTTCAAGATGCCCCAAC
Found at i:47629 original size:3 final size:3
Alignment explanation
Indices: 47621--47655 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
47611 AGAGTTCCTA
* *
47621 TTC TTC TTC TTC TTC TTC TTC TTA TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
47656 TTTTAATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:52984 original size:28 final size:28
Alignment explanation
Indices: 52948--53022 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
52938 ATTGTAAACA
52948 CCATTTTTCAACACCAACACCCACCACC
1 CCATTTTTCAACACCAACACCCACCACC
* ** *
52976 CCATTTTTCAATACTTACACCCACCATC
1 CCATTTTTCAACACCAACACCCACCACC
*
53004 TCATTTTTTCAACACCAAC
1 CCA-TTTTTCAACACCAAC
53023 CACATCACCC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 26 0.68
29 12 0.32
ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28
Consensus pattern (28 bp):
CCATTTTTCAACACCAACACCCACCACC
Found at i:54175 original size:2 final size:2
Alignment explanation
Indices: 54168--54198 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54158 TATTTAGAAA
54168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54199 AAAGTAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55984 original size:49 final size:49
Alignment explanation
Indices: 55927--56020 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
55917 ATTGATTCTC
55927 TTTTGTTTATTCTTATTGCATTTTTTCATGTATCATTGTCATATCTCAG
1 TTTTGTTTATTCTTATTGCATTTTTTCATGTATCATTGTCATATCTCAG
55976 TTTTGTTTATTCTTATTGCATTTTTTCATGTATCATTGTCATATC
1 TTTTGTTTATTCTTATTGCATTTTTTCATGTATCATTGTCATATC
56021 ACAACCTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.59
Consensus pattern (49 bp):
TTTTGTTTATTCTTATTGCATTTTTTCATGTATCATTGTCATATCTCAG
Found at i:56745 original size:17 final size:19
Alignment explanation
Indices: 56723--56761 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
56713 TGTATTTACC
56723 TTTATA-TCTT-ACTTGTT
1 TTTATACTCTTAACTTGTT
56740 TTTATACGTCTTAACTTGTT
1 TTTATAC-TCTTAACTTGTT
56760 TT
1 TT
56762 CTTTTTGCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTATACTCTTAACTTGTT
Found at i:60492 original size:2 final size:2
Alignment explanation
Indices: 60485--60525 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
60475 CATTTATCCT
60485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60526 CCATTGTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60831 original size:7 final size:7
Alignment explanation
Indices: 60831--60940 Score: 159
Period size: 7 Copynumber: 15.4 Consensus size: 7
60821 AAAAAAGAAA
60831 AAAAAAG
1 AAAAAAG
60838 AAAAAAG
1 AAAAAAG
*
60845 AGAAAAG
1 AAAAAAG
*
60852 AAGGAAA-
1 AA-AAAAG
*
60859 AAAGAAG
1 AAAAAAG
60866 AAAAAAAG
1 -AAAAAAG
60874 AAAAAAG
1 AAAAAAG
60881 AAAAAAG
1 AAAAAAG
60888 AAAAAAG
1 AAAAAAG
60895 AAAAAAG
1 AAAAAAG
60902 AAAAAAG
1 AAAAAAG
60909 AAAAAAG
1 AAAAAAG
60916 AAAAAAG
1 AAAAAAG
60923 AAAAGAAG
1 AAAA-AAG
60931 AAAAAAG
1 AAAAAAG
60938 AAA
1 AAA
60941 TTGAATCAAG
Statistics
Matches: 93, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
6 2 0.02
7 75 0.81
8 16 0.17
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:60832 original size:1 final size:1
Alignment explanation
Indices: 60821--60936 Score: 61
Period size: 1 Copynumber: 116.0 Consensus size: 1
60811 CATCCATCAG
* * * * * ** * * * *
60821 AAAAAAGAAAAAAAAAGAAAAAAGAGAAAAGAAGGAAAAAAGAAGAAAAAAAGAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
60886 AGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAGAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
60937 GAAATTGAAT
Statistics
Matches: 79, Mismatches: 36, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (1 bp):
A
Found at i:60932 original size:36 final size:36
Alignment explanation
Indices: 60831--60940 Score: 163
Period size: 36 Copynumber: 3.1 Consensus size: 36
60821 AAAAAAGAAA
* *
60831 AAAAAAGAAAAAAGAGAAAAG-AAGGAA-AAAAGAAG
1 AAAAAAGAAAAAAGAAAAAAGAAAAGAAGAAAA-AAG
60866 AAAAAAAGAAAAAAGAAAAAAGAAAA-AAGAAAAAAG
1 -AAAAAAGAAAAAAGAAAAAAGAAAAGAAGAAAAAAG
60902 AAAAAAGAAAAAAGAAAAAAGAAAAGAAGAAAAAAG
1 AAAAAAGAAAAAAGAAAAAAGAAAAGAAGAAAAAAG
60938 AAA
1 AAA
60941 TTGAATCAAG
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
35 25 0.36
36 38 0.55
37 6 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (36 bp):
AAAAAAGAAAAAAGAAAAAAGAAAAGAAGAAAAAAG
Found at i:60961 original size:14 final size:14
Alignment explanation
Indices: 60942--60976 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
60932 AAAAAGAAAT
60942 TGAATCAAGTTGGG
1 TGAATCAAGTTGGG
60956 TGAATCAAGTTGGG
1 TGAATCAAGTTGGG
*
60970 TCAATCA
1 TGAATCA
60977 TTGAGCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (14 bp):
TGAATCAAGTTGGG
Found at i:63176 original size:33 final size:33
Alignment explanation
Indices: 63134--64143 Score: 1518
Period size: 33 Copynumber: 30.3 Consensus size: 33
63124 AGGTAGATCA
* *
63134 GGATCGACATTCAAATCCATCACATAAAAAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
*
63167 GGATCGACATTCAAATCCATCACAGAAAAAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
63200 GGATCGACATTCAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
63233 GGATCGACATTCAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
*
63266 GGATCGATATTTCAAATCCATCACAGAAAGAGGT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
* * *
63300 GGATCGACATTTGAAATACATCACAGAAGGAGGT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
*
63334 GGATCGACATTCAAATCTATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
63367 GGATCGACATTCAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* *
63400 GGATCGACGTTCAAATCCATCATAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* * *
63433 GGATCGACATTCAAATCCATTATAGAAGGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
63466 GGATCGACATTTCAAATCCATCACAGAAAGAGGT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
* *
63500 GGATTGAAATTTCAAATCCATCACAGAAAGAGGT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
63534 GGATCGACATTACAAATCCATCACAGAAAGAGGT
1 GGATCGACATT-CAAATCCATCACAGAAAGAGGT
63568 GGATCGACATTTCAAATCCATCACAGAAAGAGGT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
* ** *
63602 GGAGT-GATATTTGAATCTATCACAGAAAGAGGT
1 GGA-TCGACATTCAAATCCATCACAGAAAGAGGT
*
63635 GGATCGACATTCAAATCCATCACAAAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* *
63668 GGATCGACATTTCAAATCCATCACAAAAAGAGAT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
* *
63702 GGATCGACATTTCAAATCCATCACAGAAGGAAGT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
63736 GGATCGACATTCAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* *
63769 GGATCAACATTCAAATCCATCACAGAAATAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
*
63802 GGATCGACGTTCAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
*
63835 GGATCGACATTTCAAATCCATCACAGAATGAGGT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
63869 GGATCGACATTCAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* *
63902 GGATCGACATTCAAATCCATCATAGAAAAAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* *
63935 GGAACGACATTCAAATCTATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* *
63968 GGATCGACGTTTAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* * *
64001 GAATCGACGTTCAAATCCATCACAGAAAAAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
64034 GGATCGACATTCAAATCCATCACAGAAAGAGGT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
* *
64067 GGATCGACATTTCAAATCCATCACATAAAGAGAT
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGT
* ** * *
64101 GGATCAACATTTTAATCCATCACAGAAGGAGTT
1 GGATCGACATTCAAATCCATCACAGAAAGAGGT
64134 GGATCGACAT
1 GGATCGACAT
64144 CAACTTTTTG
Statistics
Matches: 895, Mismatches: 73, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
32 1 0.00
33 585 0.65
34 306 0.34
35 3 0.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (33 bp):
GGATCGACATTCAAATCCATCACAGAAAGAGGT
Found at i:63380 original size:100 final size:101
Alignment explanation
Indices: 63134--64143 Score: 1533
Period size: 100 Copynumber: 10.1 Consensus size: 101
63124 AGGTAGATCA
* * *
63134 GGATCGACATTCAAATCCATCACATAAAAAGGTGGATCGACA-TTCAAATCCATCACAGAAAAAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
63198 GTGGATCGACA-TTCAAATCCATCACAGAAAGAGGT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
*
63233 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGATATTTCAAATCCATCACAGAAAGAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
* * *
63298 GTGGATCGACATTTGAAATACATCACAGAAGGAGGT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
*
63334 GGATCGACATTCAAATCTATCACAGAAAGAGGTGGATCGACA-TTCAAATCCATCACAGAAAGAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
* *
63398 GTGGATCGAC-GTTCAAATCCATCATAGAAAGAGGT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
* * *
63433 GGATCGACATTCAAATCCATTATAGAAGGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
* *
63498 GTGGATTGAAATTTCAAATCCATCACAGAAAGAGGT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
63534 GGATCGACATTACAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGA
1 GGATCGACATT-CAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGA
* * *
63599 GGTGGAGT-GATATTT-GAATCTATCACAGAAAGAGGT
65 GGTGGA-TCGACATTTCAAATCCATCACAGAAAGAGGT
* *
63635 GGATCGACATTCAAATCCATCACAAAAAGAGGTGGATCGACATTTCAAATCCATCACAAAAAGAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
* * *
63700 ATGGATCGACATTTCAAATCCATCACAGAAGGAAGT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
* *
63736 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCAACA-TTCAAATCCATCACAGAAATAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
*
63800 GTGGATCGAC-GTTCAAATCCATCACAGAAAGAGGT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
*
63835 GGATCGACATTTCAAATCCATCACAGAATGAGGTGGATCGACA-TTCAAATCCATCACAGAAAGA
1 GGATCGACA-TTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGA
* *
63899 GGTGGATCGACA-TTCAAATCCATCATAGAAAAAGGT
65 GGTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
* * *
63935 GGAACGACATTCAAATCTATCACAGAAAGAGGTGGATCGACGTTT-AAATCCATCACAGAAAGAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
* * *
63999 GTGAATCGAC-GTTCAAATCCATCACAGAAAAAGGT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
*
64034 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACATAAAGAG
1 GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
* * * * *
64099 ATGGATCAACATTT-TAATCCATCACAGAAGGAGTT
66 GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
64134 GGATCGACAT
1 GGATCGACAT
64144 CAACTTTTTG
Statistics
Matches: 830, Mismatches: 67, Indels: 27
0.90 0.07 0.03
Matches are distributed among these distances:
99 252 0.30
100 331 0.40
101 184 0.22
102 62 0.07
103 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (101 bp):
GGATCGACATTCAAATCCATCACAGAAAGAGGTGGATCGACATTTCAAATCCATCACAGAAAGAG
GTGGATCGACATTTCAAATCCATCACAGAAAGAGGT
Found at i:64620 original size:28 final size:28
Alignment explanation
Indices: 64546--64625 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
64536 GTAAACACTA
*
64546 TTTTAAACACCAACACCCACCACCGCAT
1 TTTTCAACACCAACACCCACCACCGCAT
** *
64574 TTTTCAACACTTACACCCACCATTC-CATT
1 TTTTCAACACCAACACCCACCA-CCGCA-T
*
64603 TTTTCAACACCAAC-CCCATCACC
1 TTTTCAACACCAACACCCACCACC
64626 CCTTGATTCC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.02
28 27 0.64
29 14 0.33
ACGTcount: A:0.31, C:0.42, G:0.01, T:0.25
Consensus pattern (28 bp):
TTTTCAACACCAACACCCACCACCGCAT
Found at i:64817 original size:17 final size:18
Alignment explanation
Indices: 64792--64825 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64782 TTTTTGAATG
64792 GATTCTAA-TCTATGTTT
1 GATTCTAATTCTATGTTT
*
64809 GATTTTAATTCTATGTT
1 GATTCTAATTCTATGTT
64826 ATTTAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.56
Consensus pattern (18 bp):
GATTCTAATTCTATGTTT
Found at i:67998 original size:3 final size:3
Alignment explanation
Indices: 67990--68095 Score: 131
Period size: 3 Copynumber: 34.3 Consensus size: 3
67980 TCGTGTTATG
67990 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
68038 TAA TAG TATA TATA TAA TAA TAG CAA TAG TAG TAG TAA TAA TAA TAA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
68085 TAA TAAA TAA T
1 TAA T-AA TAA T
68096 GGAAACGGAC
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
3 84 0.90
4 9 0.10
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:74407 original size:6 final size:6
Alignment explanation
Indices: 74396--74425 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
74386 TAACACCTTG
*
74396 TGCATT TGCATT TGCATT CGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT
74426 CTTGTTTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47
Consensus pattern (6 bp):
TGCATT
Found at i:79533 original size:257 final size:258
Alignment explanation
Indices: 79075--80908 Score: 2264
Period size: 257 Copynumber: 7.1 Consensus size: 258
79065 AGTTGTTTTG
* * **
79075 AAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAAT-ATTTTTTTTTGAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGA--AATTTTTGAA
* * * *
79139 AAATAAGAAAGCGATTTCCT-AAGTTTATTACCCAATAAACTATTTCCAAAATTGGTAAGTCCTT
64 AAGTAAGAAAGCGATTT-CTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
* * * * * * **
79203 CTGGA-CTTAAATAAGTGTTTCGAGCATGATGATTAAATCTTTCGGGTTATCTATCAGACTTTCG
128 C-GGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTCG
*
79267 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGATTTT
192 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTT
79332 AA
257 AA
* * *
79334 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTCTCAGAAAATGAAATTTTTGAAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
* *
79399 GCAAGAAAAC-ATTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
66 GTAAGAAAGCGATTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
* * *
79463 ATCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTAGAGTA
131 ACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTCGAGCA
* * *
79528 AGATGATAAGTCCTTCGGGCCATCTATAAAACCTTCGGGCAGGATATTTTCACATGATTTT-C
196 AGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAA
* ** *
79590 AAAAATGAGAAAGCGATTTTCAATGTTTCTCATTTAATGTTTTTGGAAAATGAAAATTTTGAAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
** * *
79655 GTAAGAAAATGATTTCTAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGG
66 GTAAGAAAGCGATTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
* * * *
79720 GCCATAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTT-GAGCCATCTGTCAGTCTTTT-GAG
131 ACCATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTTCGGGTCATCTGTCAGT-TTTTCGAG
* * * * * *
79783 CAAAATGATAAGTCCTTCGAGCCATCTATAAGACCTTCGGGAATGATGTTTTCACACGATTTT-C
194 CAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAA
* ** *
79847 AAAAACGAGAAAGCG-TTTTCAAAGTTTCTCATTTAAT-TTTTTGGAAAATGAAATTTTTGTAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
* * * *
79910 TTAAGAAAGCGATTTCCAAAGTTTCTTA-CTCAATAAACTATTT-CAAAGATTGGTAAGTCATTC
66 GTAAGAAAGCGATTTCTAAAGTTTCTTACCT-AGTAAACTATTTCCAAA-ATTGGTAAGTCCTTC
* * *
79973 AGG-CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTTATCTGTCAGTCTTTT-G
129 -GGACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGT-TTTTCG
* * *
80036 AGCAAGATGATAAGTCCGTCGGGCCATCTATAAGACCTTCGAGCATGATGTTTTCACATGATTTT
192 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTT
80101 AAAA
257 --AA
* * * * *
80105 AAAAACGAGAAAGCAATTTTCAAAG-TTCTCATTTAATATTTTCAGAAAATGAAAATTTTGAAAT
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
* * *
80169 GTAA-AAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCTAAAATTGGTAAGTCCTTCGG
66 GTAAGAAAGCGATTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
* * * * * * ***
80233 GCCAGT-AGTAAATCTTTCGAACTTAATGATTAAATCCTTCGGGTCATCTGTCAACCTTTCGAGC
131 ACCA-TCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTCGAGC
*
80297 AAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGA-TTTAA
195 AAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAA
*
80360 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTGAAAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
* * * *
80425 GTAAGAAAGTGATTT-TCAAAGTTTCTTACCTAGTAGACTATTTCCAAAATTTGTAAGTCATTCG
66 GTAAGAAAGCGATTTCT-AAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCG
* * * * ** *
80489 GGCCATCAGTAAGTCTTTTGAGCAAGATGATTAAATCTTTCAGGTCATCTGTCAGCCTTTCAAGC
130 GACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTCGAGC
* *
80554 AAGATGATAAGTACTTCGGGGCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTT--
195 AAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAA
* * * * ***
80616 -CAAATGAGAAAAGCAATTTTTAAAGTTTCTTATTTAATGTTTTC----AAT-TTTTTTTTGAAA
1 AAAAATGAG-AAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAA
* * *
80675 AGTAAGAAAGCGGTTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCA
65 AGTAAGAAAGCGATTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCG
* * * * * *
80740 GACCATCAGTAAGCCTTTCGAGCATGATGATTAAATCATTCGGGTCATATGTTAGTCTTTCGAGT
130 GACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTCGAGC
* * * * * *
80805 AAGATGATAAGTCCTTCGGGCCAACTATAAGACCTTTGGACAAGATGCTTTCATATGATATTTGT
195 AAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATG--ATTT-T
80870 AA
257 AA
* * *
80872 GAAAATGAGAAAGCAATTTTTAAAGTTTCTCATTTAA
1 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAA
80909 AATATTTTAA
Statistics
Matches: 1384, Mismatches: 158, Indels: 69
0.86 0.10 0.04
Matches are distributed among these distances:
251 168 0.12
252 3 0.00
253 4 0.00
254 9 0.01
255 217 0.16
256 193 0.14
257 501 0.36
258 204 0.15
259 84 0.06
260 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (258 bp):
AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAA
GTAAGAAAGCGATTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGG
ACCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTCGAGCA
AGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGATTTTAA
Found at i:79784 original size:42 final size:41
Alignment explanation
Indices: 79730--79809 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
79720 GCCATAAGTA
** *
79730 AGTCTTTCGAGCATGATGATTAAATCCTTTGAGCCATCTGTC
1 AGTCTTTCGAGCAAAATGA-TAAATCCTTCGAGCCATCTGTC
* *
79772 AGTCTTTTGAGCAAAATGATAAGTCCTTCGAGCCATCT
1 AGTCTTTCGAGCAAAATGATAAATCCTTCGAGCCATCT
79810 ATAAGACCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 17 0.52
42 16 0.48
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (41 bp):
AGTCTTTCGAGCAAAATGATAAATCCTTCGAGCCATCTGTC
Found at i:80337 original size:770 final size:766
Alignment explanation
Indices: 79070--80908 Score: 2496
Period size: 770 Copynumber: 2.4 Consensus size: 766
79060 CATTAAGTTG
* * *
79070 TTTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAATATTTTTTTT
1 TTTTCAAAAATGAGAAAGCG-TTTTCAAAGTTTCTCATTTAAT-TTTTTGGAAAATA--TTTTTT
* *
79135 TGAAAAATAAGAAAGCGATTTCCTAAGTTTATTACCCAATAAACTATTTCCAAAATTGGTAAGTC
62 TGAAAAATAAGAAAGCGATTTCCAAAGTTTCTTA-CCAATAAACTATTTCCAAAATTGGTAAGTC
* * * * * * * * *
79200 CTTCTGGACTTAAATAAGTGTTTCGAGCATGATGATTAAATCTTTCGGGTTATCTATCAGACTTT
126 CTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTTATCTGTCAGTCTTT
* *
79265 CGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGATT
191 CGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTC-GGCAAGATGTTTTCACATGATT
* * *
79330 TTAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTCTCAGAAAATGAAATTTTTG
255 TTAAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATATTCTCAGAAAATGAAAATTTTG
* *
79395 AAAAGCAAGAAAACATTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTT
320 AAAAGCAAGAAAACATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCTT
* * * * * ***
79460 CGGATCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTTAGA
385 CGGACCATCAGTAAATCTTTCGAACATAATGATTAAATCCTTCGGGTCATCTGTCAACCTTTAGA
* * **
79525 GTAAGATGATAAGTCCTTCGGGCCATCTATAAAACCTTCGGGCAGGATATTTTCACATGATTTTC
450 GCAAGATGATAAGTCCTTCGGGCCATCTATAAAACATTCGGGCAGGATATTTTCACATGATTTAA
* **
79590 AAAAATGAGAAAGCGATTTTCAATGTTTCTCATTTAATGTTTTTGGAAAATGAAAAT-TTTGAAA
515 AAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATG-AAATCTTTGAAA
79654 AGTAAGAAAATGA-TTTCTAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTC
579 AGTAAGAAAATGATTTTC-AAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTC
* * * **
79718 GGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGA-GCCATCTGTCAGTCTTTTGA
643 GGGCCATAAGTAAGTCTTTCGAGCAAGATGATTAAAT-CTTTCAGGCCATCTGTCAGCCTTTCAA
* *
79782 GCAAAATGATAAGTCCTTCGAGCCATCTATAAGACCTTCGGGAATGATGTTTTCACACGA
707 GCAAAATGATAAGTACTTCGAGCCATCTATAAGACCTTCGGGAAGGATGTTTTCACACGA
* ** *
79842 TTTTCAAAAACGAGAAAGCGTTTTCAAAGTTTCTCATTTAATTTTTTGGAAAATGAAATTTTTGT
1 TTTTCAAAAATGAGAAAGCGTTTTCAAAGTTTCTCATTTAATTTTTTGGAAAAT-ATTTTTTTGA
* *
79907 AAATTAAGAAAGCGATTTCCAAAGTTTCTTACTCAATAAACTATTT-CAAAGATTGGTAAGTCAT
65 AAAATAAGAAAGCGATTTCCAAAGTTTCTTAC-CAATAAACTATTTCCAAA-ATTGGTAAGTCCT
* * *
79971 TCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTTATCTGTCAGTCTTTTG
128 TCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTTATCTGTCAGTCTTTCG
* *
80036 AGCAAGATGATAAGTCCGTCGGGCCATCTATAAGACCTTCGAGCATGATGTTTTCACATGATTTT
193 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCG-GCAAGATGTTTTCACATGATTTT
* *
80101 AAAAAAAAACGAGAAAGCAATTTTCAAAG-TTCTCATTTAATATTTTCAGAAAATGAAAATTTTG
257 --AAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATATTCTCAGAAAATGAAAATTTTG
* * * *
80165 AAATGTAA-AAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCTAAAATTGGTAAGTCCT
320 AAAAGCAAGAAAAC-ATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCT
* * *
80229 TCGGGCCAGT-AGTAAATCTTTCGAACTTAATGATTAAATCCTTCGGGTCATCTGTCAACCTTTC
384 TCGGACCA-TCAGTAAATCTTTCGAACATAATGATTAAATCCTTCGGGTCATCTGTCAACCTTTA
* *
80293 GAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGATTT
448 GAGCAAGATGATAAGTCCTTCGGGCCATCTATAAAACATTCGGGCAGGATATTTTCACATGATTT
80358 AAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTGAA
513 AAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTGAA
* * * *
80423 AAGTAAGAAAGTGATTTTCAAAGTTTCTTACCTAGTAGACTATTTCCAAAATTTGTAAGTCATTC
578 AAGTAAGAAAATGATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTC
* * *
80488 GGGCCATCAGTAAGTCTTTTGAGCAAGATGATTAAATCTTTCAGGTCATCTGTCAGCCTTTCAAG
643 GGGCCATAAGTAAGTCTTTCGAGCAAGATGATTAAATCTTTCAGGCCATCTGTCAGCCTTTCAAG
* * * * *
80553 CAAGATGATAAGTACTTCGGGGCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGA
708 CAAAATGATAAGTACTTCGAGCCATCTATAAGACCTTCGGGAAGGATGTTTTCACACGA
* * * * * *
80612 TTTTC--AAATGAGAAAAGCAATTTTTAAAGTTTCTTATTTAATGTTTT---CAATTTTTTTTTG
1 TTTTCAAAAATGAG-AAAGC-GTTTTCAAAGTTTCTCATTTAATTTTTTGGAAAATATTTTTTTG
* * *
80672 AAAAGTAAGAAAGCGGTTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCT
64 AAAAATAAGAAAGCGATTTCCAAAGTTTCTTACC-AATAAACTATTTCCAAAATTGGTAAGTCCT
* * * * *
80737 TCAGACCATCAGTAAGCCTTTCGAGCATGATGATTAAATCATTCGGGTCATATGTTAGTCTTTCG
128 TCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTTATCTGTCAGTCTTTCG
* * * * *
80802 AGTAAGATGATAAGTCCTTCGGGCCAACTATAAGACCTTTGGACAAGATGCTTTCATATGATATT
193 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGG-CAAGATGTTTTCACATG--ATT
* *
80867 TGTAAGAAAATGAGAAAGCAATTTTTAAAGTTTCTCATTTAA
255 T-TAAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAA
80909 AATATTTTAA
Statistics
Matches: 940, Mismatches: 107, Indels: 44
0.86 0.10 0.04
Matches are distributed among these distances:
765 2 0.00
766 167 0.18
767 31 0.03
768 27 0.03
769 192 0.20
770 451 0.48
771 53 0.06
772 17 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (766 bp):
TTTTCAAAAATGAGAAAGCGTTTTCAAAGTTTCTCATTTAATTTTTTGGAAAATATTTTTTTGAA
AAATAAGAAAGCGATTTCCAAAGTTTCTTACCAATAAACTATTTCCAAAATTGGTAAGTCCTTCA
GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGGGTTATCTGTCAGTCTTTCGAGC
AAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGCAAGATGTTTTCACATGATTTTAAAA
AAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATATTCTCAGAAAATGAAAATTTTGAAAAGC
AAGAAAACATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGACC
ATCAGTAAATCTTTCGAACATAATGATTAAATCCTTCGGGTCATCTGTCAACCTTTAGAGCAAGA
TGATAAGTCCTTCGGGCCATCTATAAAACATTCGGGCAGGATATTTTCACATGATTTAAAAAAAT
GAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCTTTGAAAAGTAAGA
AAATGATTTTCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCATTCGGGCCATA
AGTAAGTCTTTCGAGCAAGATGATTAAATCTTTCAGGCCATCTGTCAGCCTTTCAAGCAAAATGA
TAAGTACTTCGAGCCATCTATAAGACCTTCGGGAAGGATGTTTTCACACGA
Found at i:80584 original size:515 final size:511
Alignment explanation
Indices: 79070--80908 Score: 2344
Period size: 515 Copynumber: 3.6 Consensus size: 511
79060 CATTAAGTTG
* ** ***
79070 TTTTGAAAAATGAGAAAGTGATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAATATTTTTTTT
1 TTTTAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAATA--AAATTT
* * * *
79135 TGAAAAATAAGAAAGCGATTTCCTAAGTTTATTACCCAATAAACTATTTCCAAAATTGGTAAGTC
64 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
* * * * * * * *
79200 CTTCTGGACTTAAATAAGTGTTTCGAGCATGATGATTAAATCTTTCGGGTTATCTATCAGA-CTT
129 CTTCGGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCA-ATCTT
79264 TCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGAT
193 TCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGAT
* *
79329 TTTAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGTATTCTCAGAAAATGAAATTTTT
258 TTTAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAT-TTTTCAGAAAATGAAATTTTT
* *
79394 GAAAAGCAAGAAA-ACA-TTTCTAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTC
322 GAAAAGTAAGAAAGAGATTTTC-AAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTC
* ** *
79457 CTTCGGATCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGGTCATCTGTCAGTTTTT
386 ATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTC-GGTCATCTGTCAGCTTTT
* * *
79522 AGAGTAAGATGATAAGTCCTTCGGGCCATCTATAAAACCTTCGGGCAGGATATTTTCACATGA
450 A-AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGA
* * * *
79585 TTTTCAAAAATGAGAAAGCGATTTTCAATGTTTCTCATTTAATGTTTTTGGAAAATGAAAATTTT
1 TTTTAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAAT-AAAATTTT
** * *
79650 GAAAAGTAAGAAAATGATTTCTAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCA
65 GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCC
* * * * *
79715 TTCGGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGAGCCATCTGTCAGTCTTTT
130 TTCGGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAATCTTTC
* * * * * *
79780 GAGCAAAATGATAAGTCCTTCGAGCCATCTATAAGACCTTCGGGAATGATGTTTTCACACGATTT
195 GAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGATTT
* * ** *
79845 T-CAAAAACGAGAAAGCG-TTTTCAAAGTTTCTCATTTAATTTTTTGGAAAATGAAATTTTTGTA
260 TAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATTTTTCAGAAAATGAAATTTTTGAA
* * * *
79908 AATTAAGAAAGCGATTTCCAAAGTTTCTTA-CTCAATAAACTATTT-CAAAGATTGGTAAGTCAT
325 AAGTAAGAAAGAGATTTTCAAAGTTTCTTACCT-AGTAAACTATTTCCAAA-ATTGGTAAGTCAT
* * * *
79971 TCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTTATCTGTCAGTCTTTTG
388 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCG-GTCATCTGTCAG-CTTTTA
* * *
80036 AGCAAGATGATAAGTCCGTCGGGCCATCTATAAGACCTTCGAGCATGATGTTTTCACATGA
451 AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGA
* * *
80097 TTTTAAAAAAAAACGAGAAAGCAATTTTCAAAG-TTCTCATTTAATATTTTCAGAAAATGAAAAT
1 TTTT---AAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAAT-AAAAT
* *
80161 TTTGAAATGTAA-AAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCTAAAATTGGTAAG
62 TTTGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAG
* * * * *
80225 TCCTTCGGGCCAGT-AGTAAATCTTTCGAACTTAATGATTAAATCCTTCGGGTCATCTGTCAACC
127 TCCTTCGGGCCA-TAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAATC
80289 TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATG
191 TTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATG
*
80354 A-TTTAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATCT
256 ATTTTAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAAT-TTTTCAGAAAATGAAATTT
* * *
80418 TTGAAAAGTAAGAAAGTGATTTTCAAAGTTTCTTACCTAGTAGACTATTTCCAAAATTTGTAAGT
320 TTGAAAAGTAAGAAAGAGATTTTCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGT
* *
80483 CATTCGGGCCATCAGTAAGTCTTTTGAGCAAGATGATTAAATCTTTCAGGTCATCTGTCAGCCTT
385 CATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTC-GGTCATCTGTCAG-CTT
* * *
80548 TCAAGCAAGATGATAAGTACTTCGGGGCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGA
448 TTAAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGA
* * * ****
80612 TTTT--CAAATGAGAAAAGCAATTTTTAAAGTTTCTTATTTAATGTTTTC----AATTTTTTTTT
1 TTTTAAAAAATGAG-AAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAATAAAATTTT
* *
80671 GAAAAGTAAGAAAGCGGTTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCC
65 GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCC
* * * * * * * *
80736 TTCAGACCATCAGTAAGCCTTTCGAGCATGATGATTAAATCATTCGGGTCATATGTTAGTCTTTC
130 TTCGGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAATCTTTC
* * * * * * * *
80801 GAGTAAGATGATAAGTCCTTCGGGCCAACTATAAGACCTTTGGACAAGATGCTTTCATATGATAT
195 GAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATG--AT
* * *
80866 TTGTAAGAAAATGAGAAAGCAATTTTTAAAGTTTCTCATTTAA
258 TT-TAAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAA
80909 AATATTTTAA
Statistics
Matches: 1147, Mismatches: 151, Indels: 55
0.85 0.11 0.04
Matches are distributed among these distances:
507 13 0.01
508 159 0.14
510 7 0.01
511 52 0.05
512 222 0.19
513 194 0.17
514 234 0.20
515 258 0.22
516 8 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (511 bp):
TTTTAAAAAATGAGAAAGCAATTTTCAAAGTTTCTCATTTAATGTTTTCGGAAAATAAAATTTTG
AAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCT
TCGGGCCATAAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAATCTTTCG
AGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGCAGGATGTTTTCACATGATTTT
AAAAAAATGAGAAAGCGATTTTCAAAGTTTCTCATTTAATTTTTCAGAAAATGAAATTTTTGAAA
AGTAAGAAAGAGATTTTCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCATTCG
GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGGTCATCTGTCAGCTTTTAAGCAA
GATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGCAGGATGTTTTCACATGA
Found at i:80937 original size:15 final size:14
Alignment explanation
Indices: 80917--80970 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
80907 AAAATATTTT
80917 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
*
80931 GAAAAAAAGAACACAA
1 -AAAAAAAGAA-AAAA
*
80947 AAAGAAAGAAAAAA
1 AAAAAAAGAAAAAA
*
80961 TAATAAAAGA
1 -AAAAAAAGA
80971 TAAAGAGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 3 0.09
15 26 0.81
16 3 0.09
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:86034 original size:19 final size:19
Alignment explanation
Indices: 85969--86035 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 19
85959 CATTCTATAT
85969 TATT-TTTTTTAATTAAAT-
1 TATTATTTTTTAA-TAAATA
*
85987 TCTTATTTTTATTGAATAAA-A
1 TATTA-TTTT-TT-AATAAATA
*
86008 GTAATATTTTTTAATAAATA
1 -TATTATTTTTTAATAAATA
86028 TATTATTT
1 TATTATTT
86036 CGGGTCAGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
18 3 0.08
19 13 0.34
20 7 0.18
21 10 0.26
22 5 0.13
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (19 bp):
TATTATTTTTTAATAAATA
Done.